def test_check_project_toplevel_dir():
with enter_temp_dir():
assert ensembler.core.check_project_toplevel_dir(
raise_exception=False) == False
ensembler.initproject.InitProject('.')
assert ensembler.core.check_project_toplevel_dir(
raise_exception=False) == True
def test_attempt_symlink_structure_files():
pdbid = '4CFE'
structure_paths = [os.path.abspath(os.path.join('tests', 'resources'))]
with enter_temp_dir():
os.mkdir('pdb')
project_pdb_filepath = os.path.join('pdb', pdbid + '.pdb.gz')
structure_type = 'pdb'
ensembler.initproject.attempt_symlink_structure_files(pdbid, '.', structure_paths, structure_type)
assert os.path.exists(project_pdb_filepath)
def test_attempt_symlink_structure_files():
pdbid = '4CFE'
structure_paths = [
get_installed_resource_filename(os.path.join('tests', 'resources'))
]
with enter_temp_dir():
os.mkdir('pdb')
project_pdb_filepath = os.path.join('pdb', pdbid + '.pdb.gz')
structure_type = 'pdb'
ensembler.initproject.attempt_symlink_structure_files(
pdbid, '.', structure_paths, structure_type)
assert os.path.exists(project_pdb_filepath)
def test_initproject():
with enter_temp_dir():
ensembler.initproject.InitProject('.')
assert os.path.exists(ensembler.core.default_project_dirnames.targets)
assert os.path.exists(ensembler.core.default_project_dirnames.templates)
assert os.path.exists(ensembler.core.default_project_dirnames.structures)
assert os.path.exists(ensembler.core.default_project_dirnames.models)
assert os.path.exists(ensembler.core.default_project_dirnames.packaged_models)
assert os.path.exists(ensembler.core.default_project_dirnames.structures_pdb)
assert os.path.exists(ensembler.core.default_project_dirnames.structures_sifts)
assert os.path.exists(ensembler.core.default_project_dirnames.templates_structures_resolved)
assert os.path.exists(ensembler.core.default_project_dirnames.templates_structures_modeled_loops)
assert os.path.exists('meta0.yaml')
def test_build_model():
template_filepath = get_installed_resource_filename(
os.path.join('tests', 'resources', 'mock_template.pdb'))
aln_filepath = get_installed_resource_filename(
os.path.join('tests', 'resources', 'mock_template-alignment.pir'))
with enter_temp_dir():
target = Mock()
template = Mock()
target_setup_data = Mock()
target.id = 'mock_target'
target.seq = 'YILGDTLGVGGKVKVGKH'
template.id = 'mock_template'
template.seq = 'YQNLSPVGSGGSVCAAFD'
target_setup_data.target_starttime = datetime.datetime.utcnow()
target_setup_data.models_target_dir = os.path.join(
ensembler.core.default_project_dirnames.models, target.id)
os.mkdir(ensembler.core.default_project_dirnames.models)
model_dir = os.path.join(
ensembler.core.default_project_dirnames.models, 'mock_target',
'mock_template')
os.makedirs(model_dir)
os.mkdir(ensembler.core.default_project_dirnames.templates)
os.mkdir(ensembler.core.default_project_dirnames.
templates_structures_resolved)
shutil.copy(
template_filepath, ensembler.core.default_project_dirnames.
templates_structures_resolved)
shutil.copy(aln_filepath, os.path.join(model_dir, 'alignment.pir'))
ensembler.modeling.build_model(target,
template,
target_setup_data=target_setup_data)
# Example model.pdb.gz contents (not testing this as it may be dependent
# upon Modeller version as well as modelling stochasticity):
#
# ..EXPDTA THEORETICAL MODEL, MODELLER 9.12 2014/08/26 13:15:44
# REMARK 6 MODELLER OBJECTIVE FUNCTION: 326.6798
# REMARK 6 MODELLER BEST TEMPLATE % SEQ ID: 27.778
# ATOM 1 N TYR 1 48.812 50.583 13.949 1.00110.28 N
# ATOM 2 CA TYR 1 49.070 50.334 15.387 1.00110.28 C
model_filepath = os.path.join(target_setup_data.models_target_dir,
template.id, 'model.pdb.gz')
assert os.path.exists(model_filepath)
assert os.path.getsize(model_filepath) > 0
def test_quick_model():
uniprot_entry_name = 'EGFR_HUMAN'
uniprot_domain_regex = '^Protein kinase'
pdbids = ['4AF3']
chainids = {'4AF3': ['A']}
with enter_temp_dir():
QuickModel(
target_uniprot_entry_name=uniprot_entry_name,
uniprot_domain_regex=uniprot_domain_regex,
pdbids=pdbids,
chainids=chainids,
loopmodel=False,
sim_length=2.0 * unit.femtoseconds,
)
assert os.path.exists(
os.path.join(default_project_dirnames.models, 'EGFR_HUMAN_D0',
'AURKB_HUMAN_D0_4AF3_A', 'explicit-refined.pdb.gz'))
def test_manual_overrides_file():
with enter_temp_dir():
ref_manual_overrides_file = get_installed_resource_filename(
os.path.join('tests', 'example_project', 'manual-overrides.yaml')
)
shutil.copy(ref_manual_overrides_file, manual_overrides_filename)
manual_overrides = ManualOverrides()
assert manual_overrides.target.domain_spans == {'ABL1_HUMAN_D0': '242-513'}
assert manual_overrides.template.min_domain_len == 0
assert manual_overrides.template.max_domain_len == 350
assert manual_overrides.template.domain_spans == {'ABL1_HUMAN_D0': '242-513'}
assert manual_overrides.template.skip_pdbs == [
'4CYJ', '4P41', '4P2W', '4QTD', '4Q2A', '4CTB', '4QOX'
]
assert manual_overrides.refinement.ph == 8.0
assert manual_overrides.refinement.custom_residue_variants_by_targetid == {
'EGFR_HUMAN_D0': {49: 'ASH'}
}
def test_quick_model():
uniprot_entry_name = "EGFR_HUMAN"
uniprot_domain_regex = "^Protein kinase"
pdbids = ["4AF3"]
chainids = {"4AF3": ["A"]}
with enter_temp_dir():
QuickModel(
target_uniprot_entry_name=uniprot_entry_name,
uniprot_domain_regex=uniprot_domain_regex,
pdbids=pdbids,
chainids=chainids,
loopmodel=False,
sim_length=2.0 * unit.femtoseconds,
)
assert os.path.exists(
os.path.join(
default_project_dirnames.models, "EGFR_HUMAN_D0", "AURKB_HUMAN_D0_4AF3_A", "explicit-refined.pdb.gz"
)
)
def test_initproject():
with enter_temp_dir():
ensembler.initproject.InitProject('.')
assert os.path.exists(ensembler.core.default_project_dirnames.targets)
assert os.path.exists(
ensembler.core.default_project_dirnames.templates)
assert os.path.exists(
ensembler.core.default_project_dirnames.structures)
assert os.path.exists(ensembler.core.default_project_dirnames.models)
assert os.path.exists(
ensembler.core.default_project_dirnames.packaged_models)
assert os.path.exists(
ensembler.core.default_project_dirnames.structures_pdb)
assert os.path.exists(
ensembler.core.default_project_dirnames.structures_sifts)
assert os.path.exists(ensembler.core.default_project_dirnames.
templates_structures_resolved)
assert os.path.exists(ensembler.core.default_project_dirnames.
templates_structures_modeled_loops)
assert os.path.exists('meta0.yaml')
assert os.path.exists(ensembler.core.manual_overrides_filename)
def test_manual_overrides_file():
with enter_temp_dir():
ref_manual_overrides_file = get_installed_resource_filename(
os.path.join('tests', 'example_project', 'manual-overrides.yaml'))
shutil.copy(ref_manual_overrides_file, manual_overrides_filename)
manual_overrides = ManualOverrides()
assert manual_overrides.target.domain_spans == {
'ABL1_HUMAN_D0': '242-513'
}
assert manual_overrides.template.min_domain_len == 0
assert manual_overrides.template.max_domain_len == 350
assert manual_overrides.template.domain_spans == {
'ABL1_HUMAN_D0': '242-513'
}
assert manual_overrides.template.skip_pdbs == [
'4CYJ', '4P41', '4P2W', '4QTD', '4Q2A', '4CTB', '4QOX'
]
assert manual_overrides.refinement.ph == 8.0
assert manual_overrides.refinement.custom_residue_variants_by_targetid == {
'EGFR_HUMAN_D0': {
49: 'ASH'
}
}
def test_build_model():
template_filepath = get_installed_resource_filename(os.path.join('tests', 'resources', 'mock_template.pdb'))
aln_filepath = get_installed_resource_filename(os.path.join('tests', 'resources', 'mock_template-alignment.pir'))
with enter_temp_dir():
target = Mock()
template = Mock()
target_setup_data = Mock()
target.id = 'mock_target'
target.seq = 'YILGDTLGVGGKVKVGKH'
template.id = 'mock_template'
template.seq = 'YQNLSPVGSGGSVCAAFD'
target_setup_data.target_starttime = datetime.datetime.utcnow()
target_setup_data.models_target_dir = os.path.join(ensembler.core.default_project_dirnames.models, target.id)
os.mkdir(ensembler.core.default_project_dirnames.models)
model_dir = os.path.join(ensembler.core.default_project_dirnames.models, 'mock_target', 'mock_template')
os.makedirs(model_dir)
os.mkdir(ensembler.core.default_project_dirnames.templates)
os.mkdir(ensembler.core.default_project_dirnames.templates_structures_resolved)
shutil.copy(template_filepath, ensembler.core.default_project_dirnames.templates_structures_resolved)
shutil.copy(aln_filepath, os.path.join(model_dir, 'alignment.pir'))
ensembler.modeling.build_model(target, template, target_setup_data=target_setup_data)
# Example model.pdb.gz contents (not testing this as it may be dependent
# upon Modeller version as well as modelling stochasticity):
#
# ..EXPDTA THEORETICAL MODEL, MODELLER 9.12 2014/08/26 13:15:44
# REMARK 6 MODELLER OBJECTIVE FUNCTION: 326.6798
# REMARK 6 MODELLER BEST TEMPLATE % SEQ ID: 27.778
# ATOM 1 N TYR 1 48.812 50.583 13.949 1.00110.28 N
# ATOM 2 CA TYR 1 49.070 50.334 15.387 1.00110.28 C
model_filepath = os.path.join(target_setup_data.models_target_dir, template.id, 'model.pdb.gz')
assert os.path.exists(model_filepath)
assert os.path.getsize(model_filepath) > 0
def test_check_project_toplevel_dir():
with enter_temp_dir():
assert ensembler.core.check_project_toplevel_dir(raise_exception=False) == False
ensembler.initproject.InitProject('.')
assert ensembler.core.check_project_toplevel_dir(raise_exception=False) == True
